(Name, Address and Telephone Number of Person Authorized to Receive Notices and Communications)

September 25, 2018

(Date of Event which Requires Filing of this Statement)

If the filing
person has previously filed a statement on Schedule 13G to report the acquisition which is subject of this Schedule 13D, and is filing this statement because of Rule 13d-1(e),13d-1(f) or 13d-1(g), check the following box. ☐

Note: Schedules filed in
paper format shall include a signed original and five copies of the schedule, including all exhibits. See Rule 13d-7(b) for other parties to whom copies are to be sent.

*

The remainder of this cover page shall be filled out for a reporting persons initial filing on this form
with respect to the subject class of securities, and for any subsequent amendment containing information which would alter disclosures provided in a prior cover page.

The information required on the remainder of this cover page shall not be deemed to be filed for the purpose of Section 18 of
the Securities Exchange Act of 1934 (the Act) or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act (however, see the Notes).

CUSIP No.: 92686J106

1.

Name of
Reporting Person:

Ligand Pharmaceuticals Incorporated

2.

Check the Appropriate Box if a Member
of Group (See Instructions):

(a) ☐ (b) ☐

3.

SEC Use Only:

4.

Source of Funds:

WC and OO

5.

Check if Disclosure of Legal
Proceedings is Required Pursuant to Items 2(d) or 2(e):

☐

6.

Citizenship or Place of
Organization:

Delaware

Number of

Shares

Beneficially

Owned By

Each

Reporting

Person

With:

7.

Sole Voting Power:

0

8.

Shared Voting Power:

7,558,083

9.

Sole Dispositive Power:

0

10.

Shared Dispositive Power:

7,558,083

11.

Aggregate Amount Beneficially Owned by Each Reporting Person:

7,558,083

12.

Check if the Aggregate Amount in Row
(11) Excludes Certain Shares:

☐

13.

Percent of Class Represented By Amount
In Row (11):

10.4%

14.

Type of Reporting Person:

CO

2

Preliminary Note

This Amendment No. 3 to Schedule 13D (this Amendment No. 3) amends and supplements the Schedule 13D filed with the
United States Securities and Exchange Commission (the SEC) on May 8, 2015 and as previously amended (the Schedule 13D) by Ligand Pharmaceuticals Incorporated (Ligand or the Reporting Person).
Capitalized terms used but not defined herein shall have the meaning given in the Schedule 13D.

Item 4.

Purpose of Transaction

Item 4 is hereby amended and restated by the following:

Ligand and the Issuer were previously parties to a Loan and Security Agreement, dated May 21, 2014 (as amended by the First Amendment to
Loan and Security Agreement, dated April 8, 2015, and the Second Amendment to Loan and Security Agreement, dated January 22, 2016, the Loan and Security Agreement), pursuant to which Ligand loaned $2,500,000 to the Issuer. Such
debt was evidenced by a Senior Convertible Promissory Note (the Convertible Note).

Pursuant to the terms of the Loan and
Security Agreement, upon the consummation of the Follow-On Public Offering on April 13, 2016, the Issuer repaid Ligand $1,500,000, which payment was comprised of $300,000 in cash, with the balance of the
$1,500,000 paid in the Issuers equity securities, resulting in the issuance of 960,000 shares of Common Stock to Ligand in the Follow-On Public Offering. Such payment was applied, first, to accrued and
unpaid interest on the Convertible Note and, second, to the unpaid principal amount of the Convertible Note. On July 15, 2017, the Issuer repaid Ligand an additional $200,000 in cash. Such payment was applied, first, to accrued and unpaid
interest on the Convertible Note and, second, to the unpaid principal amount of the Convertible Note. On May 23, 2018, the Convertible Note was repurchased in full by the Issuer for $3,876,937 in cash. The Convertible Note and Loan and Security
Agreement are no longer outstanding.

In addition, Ligand holds warrants to purchase up to 1,520,000 shares of Common Stock (the
Warrants). The Warrants have an exercise price of $1.50 per share of Common Stock and are immediately exercisable. The Warrants expire on April 13, 2021.

On September 25, 2018, Ligand sold 262,881 shares of Common Stock at a weighted average price of $19.1503 in open market transactions on
the Nasdaq Capital Market. Such shares of Common Stock were sold in multiple transactions at prices ranging from $19.00 to $19.74, inclusive.

On September 28, 2018, Ligand entered into a Trading Plan (the Trading Plan) pursuant to Rule
10b5-1 under the Securities Exchange Act of 1934, as amended. Pursuant to the Trading Plan, a broker dealer may make periodic sales of Common Stock on behalf of Ligand, in specified amounts at market prices
subject to specified limitations. This description of the Trading Plan does not purport to be complete and is qualified in its entirety by the text of the Trading Plan, the form of which is attached as Exhibit 99.13 to this Schedule 13D
and is incorporated herein by reference.

Ligand acquired the securities described in this Schedule 13D for investment purposes and
intends to review its investments in the Issuer on a continuing basis. Any actions Ligand might undertake will be dependent upon the its review of numerous factors, including, but not limited to: an ongoing evaluation of the Issuers business,
financial condition, operations and prospects; price levels of the Issuers securities; general market, industry and economic conditions; the relative attractiveness of alternative business and investment opportunities; and other future
developments.

Ligand may, at any time and from time to time, acquire additional securities of the Issuer, or retain or sell all or a
portion of the securities then held, in the open market or in privately negotiated transactions. In addition, Ligand may engage in discussions with management, the board of directors, and shareholders of the Issuer and other relevant parties or
encourage such persons to consider or explore extraordinary corporate transactions, such as: a merger; sales or acquisitions of assets or businesses; changes to the capitalization or dividend policy of the Issuer; or other material changes to the
Issuers business or corporate structure.

Other than as described above, Ligand does not have any plans or proposals that relate to,
or would result in, any of the matters listed in Items 4(a)(j) of Schedule 13D, although, depending on the factors discussed herein, the Reporting Persons may change their purpose or formulate different plans or proposals with respect thereto
at any time.

3

Item 5.

Interest in Securities of the Issuer

Item 5 is hereby amended and restated by the following:

(a) - (b) Ligand beneficially owns, in the aggregate, 7,558,083 shares of Common Stock, constituting approximately 10.6% of the Common Stock
outstanding, consisting of (i) 5,155,609 shares of Common Stock held directly by Ligand, (ii) 882,474 shares of Common Stock held directly by Metabasis, and (iii) 1,520,000 shares of Common Stock issuable upon exercise of the Warrants held directly
by Ligand.

The aggregate percentage of Common Stock beneficially owned by Ligand is based on 72,979,857 shares outstanding, consisting of
(i) 71,459,857 shares of Common Stock outstanding as of October 31, 2018, as reported in the Issuers quarterly report on Form 10-Q filed with the Securities and Exchange Commission on
November 7, 2018, and (ii) 1,520,000 shares of Common Stock issuable upon exercise of the Warrants.

(c) Except for the transactions
disclosed in Item 4 above, Ligand has not effected any transactions in the class of securities reported during the past 60 days.

(d) None.

(e) Not applicable.

Item 6.

Contracts, Arrangements, Understandings or Relationships with Respect to Securities of the Issuer

Item 6 is hereby amended and supplemented by the following:

Item 4 above summarizes certain provisions of the Trading Plan and is incorporated herein by reference. A copy of the Trading Plan is filed as
an exhibit to this Amendment No. 3, and is incorporated by reference herein. The description of the Trading Plan is incorporated herein by reference to Item 4.

Incorporated by reference to Exhibit 99.1 to the Reporting Persons Schedule 13, as filed with the Securities and Exchange Commission on May 8, 2015 (SEC Reg.
No. 005-88828)

99.2

Form of Lock-Up Agreement among the Company, the Underwriters and Certain Stockholders of the Company

Incorporated by reference to Exhibit A to Exhibit 1.1 to the Issuers Amendment No. 5 to Registration Statement on Form S-1, as filed with the Securities and Exchange Commission on
April 10, 2015 (SEC Reg. No. 333-197182)

Incorporated by reference to Exhibit 10.12 to the Issuers Registration Statement on Form S-1, as filed with the Securities and Exchange Commission on July 1, 2014 (SEC Reg. No. 333-197182)

4

99.4

First Amendment to Master License Agreement, dated September 6, 2014, by and among Viking Therapeutics, Inc., Metabasis Therapeutics, Inc. and Ligand Pharmaceuticals Incorporated

Incorporated by reference to Exhibit 10.24 to the Issuers Amendment No. 2 to Registration Statement on Form S-1, as filed with the Securities and Exchange Commission on
April 10, 2015 (SEC Reg. No. 333-197182)

99.5

Second Amendment to Master License Agreement, dated April 8, 2015, by and among Viking Therapeutics, Inc., Metabasis Therapeutics, Inc. and Ligand Pharmaceuticals Incorporated

Incorporated by reference to Exhibit 10.30 to the Issuers Amendment No. 5 to Registration Statement on Form S-1, as filed with the Securities and Exchange Commission on
September 8, 2014 (SEC Reg. No. 333-197182)

99.6

Loan and Security Agreement, dated May 21, 2014, by and between Viking Therapeutics, Inc. and Ligand Pharmaceuticals Incorporated

Incorporated by reference to Exhibit 10.13 to the Issuers Registration Statement on Form S-1, as filed with the Securities and Exchange Commission on July 1, 2014 (SEC Reg. No. 333-197182)

99.7

First Amendment to Loan and Security Agreement, dated April 8, 2015, by and between Viking Therapeutics, Inc. and Ligand Pharmaceuticals Incorporated

Incorporated by reference to Exhibit 10.31 to the Issuers Amendment No. 5 to Registration Statement on Form S-1, as filed with the Securities and Exchange Commission on
April 10, 2015 (SEC Reg. No. 333-197182)